Enterprise has been in the Delphic Expanse for six weeks and have yet to get any intel about the Xindi. Strange anomalies affect the ship, sending cargo flying violently through the bays, pockets of atmosphere losing gravity and other incidents defying the known laws of physics. T'Pol helps Trip's insomnia with an intimate Vulcan therapy. Archer and Trip find another race of Xindi imprisoned in a mine.

Enterprise is damaged by spatial anomalies and boarded by interstellar pirates who rob the ship of critical resources.

Archer, Reed, and Sato are threatened by a virus that mutates them into a primal lifeform.

Enterprise helps an alien woman, Rajiin, seeking to escape her life as a sex slave. Once on board she uses her alien abilities to gather biometric data about humans and is recaptured by her employers, the Xindi council.

Enterprise answers a distress signal from a stranded Vulcan ship, only when arriving they find the ship completely desolate, wrecked - and filled with Vulcan zombies.

Hoshi Sato is contacted by a 400-year-old telepathic alien exiled on planet in the Expanse, shunned by his society because of his abilities. The alien offers to use his powers to help Enterprise find the Xindi and the weapon they are building, but only if Hoshi will stay with him while he works. She agrees to stay behind, while Enterprise confirms the Expanse has a second Sphere and is on its way to investigate.

Enterprise discovers a Xindi mining outpost where components of the Xindi weapon are being assembled.

His memory crippled, Archer awakens years in the future, after the Xindi have reduced Earth to a cinder and the remnants of humanity have settled on a distant planet. Now, Archer learns that he may be the key to undoing this tragedy.

Enterprise investigates a previously unknown colony of humans who are living in the fashion of the American Old West. They are oppressing an alien race called the Skagarans.

Archer decides to make a fast-growing clone of Trip to help save his life while Enterprise is stranded in a dangerous field with nucleonic particles.

Archer and T'Pol travel back in time to Detroit in 2004 to stop three Xindi-Reptilians from constructing a bioweapon.

Enterprise is taken over by religious zealots, who worship the mysterious spheres in the Expanse. they want to use the ship in a war against heretics.

Enterprise has found the location of the testing site of the Xindi weapon and gets some rather unexpected help.

Enterprise captures Degra, the mastermind behind the Xindi weapon project, and Archer tries to trick him into revealing the location of the final weapon.

With Reed and Hayes fighting over a training program and Trip seemingly making T'Pol jealous, Enterprise discovers a dying alien in a pod with technology similar to the Spheres.

While in command of Enterprise because the entire crew is in a coma, Dr. Phlox starts hearing some strange sounds.

Enterprise finds a derelict Xindi-Insectoid starship carrying a cache of unhatched eggs and Archer takes an increasingly obsessive interest in preserving them.

Archer decides he should pilot a kamikaze shuttle to destroy the Xindi weapon. Temporal agent Daniels urges him to reconsider.

Captain Archer has been returned to Enterprise by the Xindi council awaiting a hearing. But after a heavy attack by the Reptilians, Enterprise is stranded without a functional warp drive. They meet another ship in trouble because of space anomalies. The ship's captain isn't willing to trade in their warp coil and Archer must make a tough decision. Meanwhile T'Pol is having some strange sensations and can't control her emotions.

Two members of the Xindi Council offer to stop the launch of the weapon if Archer can prove that the Xindi have been manipulated; the crew holds a memorial for their dead shipmates.

Trying to pass through a subspace corridor, Enterprise is stopped by a version of itself from the future.

Enterprise has arrived at the location of the Xindi Council and with the help of Degra, Archer can make his plea in front of the five races of Xindi. Archer needs to prove that the Sphere Builders have been telling lies. While the Primates and Arboreals are already aware of the truth, convincing the other three races will not be easy. The Reptilians and Insectoids refuse to even listen to Archer. Meanwhile, the Sphere Builders haven't been sitting still, and have arranged a secret meeting with the Reptilians.

While the Reptilians force Hoshi to decipher a launch code, the Primates, Arboreals and Archer think of a way to stop the Xindi weapon.

Archer takes Degra's ship to try to prevent Earth from being destroyed and gets some unexpected help. Enterprise tries to destroy Sphere 41, but the Sphere Builders know about the plan.